Ontology
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Ontology Refinement with Embeddings and LLMs: A Case Study on CASTON
2026-10-15 08:10:05Hui Yang, Ziyu Li, Xuan Liu, Anders Jarfors, He Tan, Jiaoyan ChenAbstract
Ontologies are widely used to represent and organize complex knowledge in domains such as biomedicine and healthcare. However, constructing reliable ontologies remains challenging, as class hierarchies, whether manually or automatically constructed, may contain subtle subsumption errors that require careful refinement. We study this problem in CASTON, a casting-domain ontology, and present a lightweight but scalable refinement workflow that combines a fine-tuned ontology embedding model with Large Language Models (LLMs). The embedding model is used to extract a limited number of candidate axioms for refinement together with possible replacement candidates, and an LLM then returns repair suggestions. In a small expert evaluation, the default configuration using a CASTON-fine-tuned OnT embedding model and Qwen3-8B produced reliable high-confidence repairs: all six high-confidence replacements were accepted by both domain experts. The implementation is available at this https URL.
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https://arxiv.org/abs/2610.21466
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Steering Vectors for Competing Ethical Frameworks Are Interchangeable: A Competing-Target Test for Activation Steering
2026-10-14 01:00:35Weilun Xu (EPFL), Zipeng Sun (McGill University,Mila)Abstract
Activation steering adds a vector to a model's hidden states to control a named behaviour. A gain on that behaviour, however, does not show that the vector controls it directly: it may act through a component shared with neighbouring behaviours, which unsteered and random baselines cannot separate. We introduce the competing-target test: a vector is compared with the vector built the same way for a competing target, and an equivalence test states when their difference is below a useful margin. We apply it in open-weight models to vectors for Kantian deontology, which judges an act by the rule it follows, and act utilitarianism, which judges it by the welfare it produces. On held-out situations, prompting a framework raises its score and lowers the other's, whereas vectors for either framework move both scores alike, and none reaches the margin. The two vectors share most of their direction, a request to apply some framework; the same construction separates an optimistic from a pessimistic tone, whose vectors share much less. What a vector shares with its competitors therefore sets what it controls: steering a perspective can deliver a mixture, and measuring a disposition can measure its neighbours, unless tested against the competing target.
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https://arxiv.org/abs/2610.19359
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From Qualitative Text to Integrated Evidence: The Parallel-Then-Integrated Procedure
2026-10-13 20:29:58Elyas Irankhah, Ashley Hagaman, Samah FodehAbstract
Mixed methods research offers established strategies for integrating qualitative and quantitative evidence, but less guidance for integrating two computational representations of the same qualitative corpus. This methodological study introduces Parallel-Then-Integrated (PTI), a four-step procedure for explicit and traceable integration. We present PTI using 1,203 interview paragraphs from 29 mothers in Nepal. The two representations were ontology-guided Patient Voice (PV) coding with PVminer and data-driven themes generated through non-negative matrix factorization (NMF). A theme-complete crosswalk documented convergence, divergence, and preprocessing-sensitive differences. Depression status, based on Patient Health Questionnaire-9 (PHQ-9) scores, served as a secondary external anchor for exploratory association checks. PTI provides a structured approach for integrating computational representations of qualitative text within mixed methods research.
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https://arxiv.org/abs/2610.19164
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Plant Memory: Technical Language Processing and a Verified Maintenance Ontology for Agent-Accessible Failure Knowledge from SAP PM Work Orders
2026-10-13 20:02:31Akash RajAbstract
Maintenance work orders are the largest written record of how industrial equipment fails, yet in most plants they are close to unusable for analysis. Short texts are abbreviated and misspelt, asset identity is buried in free text, work-type labels contradict the work described, and the fields that matter most for reliability (symptom, root cause, action taken) are usually empty. As a result, diagnostic knowledge stays with senior technicians and leaves when they do. We present Plant Memory, a system that applies technical language processing (TLP) to SAP Plant Maintenance (PM) exports and builds an ISO 14224-aligned maintenance ontology in which every extracted statement is a reified fact carrying a confidence score, the evidence it was read from, and a verification state. Extraction is rule-first, with an optional large language model (LLM) acting as a second reader whose disagreements raise a fact's review priority rather than overwrite it. Technicians verify facts through a review queue, answer targeted knowledge-gap questions where failures repeat without a recorded cause, and approve or reject ontology drift proposals when new terms appear. The resulting graph is served to people through a web application and to AI agents through a Model Context Protocol (MCP) server, so both query the same verified knowledge and every answer cites the work orders behind it. On a synthetic 12-month export of 400 work orders from a parboiled-rice plant, rule-based extraction reaches 96.2% component accuracy, 88.9% failure-mode accuracy and 100% root-cause precision at 62% coverage; on 28 diagnostic questions, ranked root causes from the ontology are correct at top-1 in 82.1% of cases against 53.6% for the raw SAP root-cause column.
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https://arxiv.org/abs/2610.19131
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SMI: Ontology-Grounded Semantic IDs for Hierarchy-Aware Medical Concept Representation
2026-10-13 16:30:01Ziyang Song, Lia Shen, Yixuan Li, Qincheng Lu, Weihao Li, Haoran Xu, He Zhu, Xinyu Wang, Yue LiAbstract
Biomedical language models (LMs) provide strong representations for clinical tasks, but they often fail to capture the hierarchical structure among medical concepts. This limitation is especially pronounced for rare and fine-grained clinical codes in long-tailed vocabularies, where hierarchy-agnostic LM representations become less informative as concept frequency decreases. We introduce Semantic Medical Identifier (SMI), a training-free framework for constructing ontology-grounded Semantic IDs and hierarchy-aware medical concept representations. For each diagnosis, procedure, or medication concept, SMI defines its Semantic ID as the coarse-to-fine path through an expert-defined medical ontology. SMI then aggregates frozen biomedical LM embeddings across the corresponding ontology levels to form hierarchy-aware medical concept representations that preserve coarse-to-fine clinical semantics. The base SMI uses uniform aggregation across ontology levels, while a level-weighted variant selects global level weights on validation data. Our theoretical analysis shows that SMI yields more informative medical concept representations than hierarchy-agnostic LM embeddings, particularly for rare and fine-grained clinical concepts. Experiments show that SMI captures meaningful hierarchical structure and improves clinical relation prediction. On MIMIC-IV, SMI improves mortality prediction, readmission prediction, drug recommendation, and rare drug prediction. On eICU, SMI yields more robust patient representations under cross-hospital distribution shift.
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https://arxiv.org/abs/2610.18672
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EventLens: Event-Structure Reinforcement Learning for Video Understanding
2026-10-12 04:46:04Guowen Zhang, Boshen Xu, Zihao Yue, Ziheng Wang, Xiaokun Liu, Xin Tao, Wenyu Qin, Pengfei Wan, Qin JinAbstract
Recent multimodal large language models (MLLMs) achieve strong results on video question answering, yet often fail to recover the temporal structure that makes a video coherent. They may merge neighboring events, miss single-event progression, or infer implausible relations across events. We study structured temporal understanding as the ability to recover event structure from visual evidence, including event boundaries, single-event progression, and multi-event relations. We argue that this gap arises from a mismatch between current post-training objectives and temporal reasoning, where caption-style supervision allows models to rely on language shortcuts rather than visual temporal grounding. To address this, we propose EventLens, a vision-centric reinforcement learning framework that learns video understanding through event-structure recovery. Instead of reconstructing captions, EventLens trains models to recover temporal structure under controlled perturbations, such as altered temporal granularity, reversed progression, and shuffled event order. We instantiate this framework with a three-level temporal ontology and derive three verifiable task families: event segmentation, progression discrimination, and multi-event relation reasoning. These tasks admit deterministic rewards, enabling task-specialized GRPO training without human preference labels or learned reward models. We further introduce multi-teacher on-policy distillation (MT-OPD) to consolidate specialized policies into a unified model. Experiments on Qwen3-VL backbones show consistent improvements on temporal grounding and event-sensitive reasoning benchmarks, while preserving general video-QA performance. Learning curves further demonstrate that EventLens achieves comparable downstream transfer with significantly reduced training cost compared to direct mixed RL optimization.
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https://arxiv.org/abs/2610.16172
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LURE: a Phase-Labelled Synthetic Corpus of Online-Grooming Exchanges
2026-10-11 20:41:08Emanuele Florindi, Valentina Franzoni, Ludovico Guercio, Alfredo Milani, Mattia PolticchiaAbstract
Phase-annotated conversational data is essential for studying the progression of online grooming of minors and for developing early warning tools. However, the only publicly available source (i.e., Perverted-Justice archive, which contains a subset coded using ChatCoder) is small, outdated, and frozen. We present a synthetic corpus of groomer-victim exchanges, generated using a retrieval-augmented pipeline running on institutional hardware. This pipeline uses an openly available, eight-billion-parameter, refusal-ablated language model. The corpus was created using the five stages of the responsible-generation protocol for synthetic datasets: ontology-driven design based on the ChatCoder luring-communication scheme (eight communicative tags mapped onto four grooming phases); multi-model prompt testing; human-in-the-loop supervision; semantic and feature-level validation; and modality-aware documentation. The released corpus contains 2,121 unique exchanges across seven tags and four phases, each accompanied by a Plutchik emotion field. Validation quantifies the integrity and lexical profile of the corpus, as well as the reproduction of real seed lines, in-domain label recoverability (tag accuracy: 0.85; phase accuracy: 0.93) and its transfer to real ChatCoder offender lines, which were coded automatically at the eight-tag level (31,640 lines) and by human coders at the three-construct level (10,876 posts). Accuracy was measured for lexical and sentence-embedding features, while a real-versus-synthetic discriminator was able to separate the two domains with 91% accuracy. The scope of the corpus includes controlled, phase-conditioned experimentation, pipeline development and augmentation alongside real data and awareness material. The corpus, its datasheet and the audit code are released with vetted access.
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https://arxiv.org/abs/2610.15908
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Gugak-VocalSet: A Multi-Genre Studio-Quality Dataset of Korean Traditional Singing with Sigimsae Annotations
2026-10-11 05:14:13Danbinaerin Han, Wonil Kim, Seah Hong, Dongjoo Moon, Jaeok Lee, Jongpil Lee, Chaewon Kim, Juhan NamAbstract
We present Gugak-VocalSet, the first publicly available audio dataset for Korean traditional singing with dense annotations of sigimsae, a structured pitch contour system of vocal expressions. Gugak-VocalSet contains 24.5 hours of unaccompanied solo vocal recordings across 305 tracks of representative repertoire curated by the National Gugak Center, performed by 20 professional singers in a controlled studio environment with fixed key and tempo. In addition to genre, lyrics, and mood/timbre tags, the dataset provides a unified sigimsae ontology and approximately 68,000 segments (71,700 instances including multi-label) of audio-grounded sigimsae annotations; the ontology adopts a functional-position-based hierarchy designed for consistent application across genres, and 14 expert annotators specializing in Korean traditional music performed segment-level labeling accordingly. Baseline experiments on sigimsae classification and event detection show that domain-informed F0 representations remain competitive with, and on classification surpass, frozen probing of a general-purpose music foundation model, while pitch and spectral cues play complementary roles in event-level detection. Companion page: this https URL
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https://arxiv.org/abs/2610.15350
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OntoAR-HAR: Ontology-Guided Agentic RAG with Personalized Memory for Human Activity Recognition
2026-10-11 02:57:12Xiangqing Lu, Tao Zhu, Liang Yu, Shuangjian Li, Lulu Ban, Furong Duan, Mingxing Nie, Liming Chen, Yaping WanAbstract
LLMs increasingly support sensor-based human activity recognition (HAR) by linking motion signals with activity semantics and physical knowledge. Retrieval-augmented generation (RAG) grounds decisions in sensor examples and domain features, enabling training-free target-user inference with less dependence on raw numerical arrays. However, existing LLM/RAG-based HAR typically searches single-level activity spaces using static population knowledge. Consequently, they compare many unrelated candidates using the same static population evidence and overlook personalized motion patterns. We propose OntoAR-HAR, an ontology-guided agentic RAG framework combining static population and personalized knowledge. Its tree-structured activity ontology decomposes classification into local decisions among semantically related activities. The static store supplies node-constrained examples, while offline-discovered executable signal features provide numerical evidence for local distinctions. During inference, the personalized store collects selected user observations, which the LLM integrates with static knowledge and signal features while traversing the ontology to an activity label. Cross-subject and heterogeneous-sensing experiments show complementary gains from hierarchical retrieval and personalized memory across multiple LLM backbones, achieving state-of-the-art performance. By explicitly modeling hierarchical relations across activity granularities, OntoAR-HAR also addresses the long-overlooked semantic inclusion problem and avoids treating related labels as independent categories.
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https://arxiv.org/abs/2610.15292
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scHFBiMamba: a bidirectional Mamba autoencoder for cardiac disease-state classification from single-nucleus RNA-seq data
2026-10-10 18:47:11Ugo Lomoio, Pietro Hiram Guzzi, Pierangelo VeltriAbstract
To evaluate whether a compact bidirectional state-space autoencoder improves joint classification of species, cell type, and disease state from single-nucleus RNA-sequencing profiles in heart failure (HF), while yielding interpretable gene attributions. Building on the dense denoising autoencoder (DAE) and MLP framework of Ruz Jurado et al., we developed scHFBiMamba, combining a bidirectional Mamba autoencoder (BiMambaAE) with an MLP head. BiMambaAE maps 16,545-gene profiles to 350-dimensional latent representations using 13.2M parameters, about 14.6-fold fewer than the dense DAE (192.9M). We compared six encoder-classifier configurations on 38,275 held-out cardiac nuclei using McNemar tests with Benjamini-Hochberg correction, and assessed nine classifiers on frozen representations. Biological relevance was evaluated by comparing SHAP-derived differentially explained genes with differentially expressed genes against curated HF-related Gene Ontology keywords. BiMambaAE+MLP achieved the highest aggregate F1: pooled macro-F1 across 13 outputs was 0.966 versus 0.957 for DAE+MLP, and the mean category macro-F1 was 0.977 versus 0.970. It significantly improved cell-type and disease-state accuracy (adjusted p=7.1e-3 and p=4.8e-6, respectively), with species F1 of 1.000. SHAP-derived differentially explained genes achieved a pathway-enrichment benchmark F1 of 0.105 versus 0.053 for differentially expressed genes. Compact bidirectional state-space autoencoders can outperform substantially larger dense autoencoders for joint cardiac transcriptomic classification while reducing parameters. scHFBiMamba enables accurate multi-task prediction and hypothesis-generating gene-level interpretation. Code: this https URL.
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https://arxiv.org/abs/2610.15117
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ScienceBuddy-PV: A Verifier-Governed Recursive Improvement Protocol for Panvascular Intervention Research
2026-10-10 03:35:28Lingsen You, Yujun Guo, Xinyu Zhong, Zijie Feng, Wentong Wang, Li Shen, Junbo GeAbstract
ScienceBuddy-PV adapts the ScienceBuddy recursive-in-recursive design to panvascular intervention research through a structured evidence ledger, device-vessel ontology, abstention contract and retained failure bank. Recursive harness optimization and outer-loop model learning, including reinforcement learning, are specified but not executed. We audit a fixed component, rather than the complete agent system, using separate ARCADE syntax and stenosis tasks (1,000 training, 200 validation and 300 test images per task). A shared task-masked convolutional model was trained once per representation setting; its parameters and the heuristic support gate were then held fixed, with the stenosis threshold selected on validation data. On the locked test sets, syntax Dice was 0.475 (95% CI 0.459-0.490) and stenosis Dice was 0.231 (95% CI 0.214-0.249). Stenosis pixel AUROC was 0.957 and AUPRC was 0.180 at prevalence 0.00975. The gate accepted 76.7% of stenosis-frame outputs versus 100% for a score-only comparator. In a constructed mask audit, it accepted 44.3% of reference candidates and rejected 55.7%, exposing the cost of abstention. Acceptance does not establish correctness or clinical safety. This public-data component audit makes support and abstention measurable and provides a reproducible protocol for future collaborative agent studies. It does not demonstrate recursive improvement, patient-level validity or clinical device recommendations.
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https://arxiv.org/abs/2610.14523
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Speech event detector: Timestamped detection of non-verbal vocalizations and background sounds for rich speech transcription
2026-10-09 18:49:55Ayush Kumar Bar, Promila GhoshAbstract
Automatic speech recognition produces words but drops the non-verbal content of a recording: the breaths, coughs, sighs and laughter of the speaker, and the horns, music or barking around them. We describe Speech Event Detector, a 5.8-million-parameter convolutional-Transformer model that outputs probabilities every 40 ms for 54 event classes (20 speaker vocalizations and 34 background sounds), together with post-processing that converts these probabilities into timestamped events and a procedure for merging the events into a Whisper transcript. The model is trained on material drawn from seven public datasets whose labels come in incompatible forms: single detected regions, free-text tags with timestamps, temporally strong ontology labels, symbols embedded in transcripts, isolated recordings and environmental recordings. We unify them using rule-based label mapping, recover timestamps for transcript-embedded labels through CTC forced alignment, locating 6,360 of 8,620 sounds, and combine about 168 hours of real annotated training recordings with synthetic mixtures and augmentation using real background noise. Per-class thresholds for two operating profiles are tuned on real held-out recordings, and performance is estimated using two-fold cross-validation. On whole held-out recordings from four datasets, considering the 48 classes with at least ten held-out events, the sensitive profile detects an average of 49 percent of a class's events, covering 67 percent of all 9,367 events, at a macro precision of 0.30. The balanced profile achieves a macro recall of 0.37 at a precision of 0.36, with macro event F1 scores of 0.32 and 0.33, respectively. The detector runs about 39 times faster than real time on eight CPU threads.
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https://arxiv.org/abs/2610.14232
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U4RASD at KnowledgeGraphEval-2026: Ontology-Constrained Encoder and LLM Systems for Arabic Relation Extraction
2026-10-08 21:41:29Ahmad Abbas, Hussein Mazeh, Chadi Abou Chakra, Aya Jouni, Mohammad Ballout, Fadi A. ZaraketAbstract
This paper details our submission to KnowledgeGraphEval 2026 Subtask 2 on directed Arabic relation extraction. We explored encoder-based and large language model approaches for predicting one of 40 relations or no_relation from an Arabic sentence and a subject-object pair. Our encoder systems use typed entity markers and separate relation-existence and relation-classification heads, while our LLM systems fine-tune Yehia and Qwen3.5 with QLoRA and ontology-constrained prediction. Our best system, an ensemble of Yehia-RE, Qwen-RE, and TypedPair, achieved a micro-F1 score of 94.06 and ranked 1st in Subtask 2. Yehia-RE (full-vocabulary) achieved 92.98, while the best encoder and Qwen-RE achieved 92.69 and 91.94 respectively. Our results highlight the importance of constrained prediction and complementary modeling approaches for Arabic relation extraction.
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https://arxiv.org/abs/2610.12742
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CLUE: A Contrastive Learning Framework for Unsupervised Event Type Induction and Annotation
2026-10-08 18:05:16Pratik Maitra, Lauren Kwon, Qi LiAbstract
Event ontology is the foundational framework for defining events in a dataset. Event type induction generally involves domain experts who define guidelines for creating event types and their names based on the dataset's domain and scope. However, this process is resource-intensive in terms of annotation costs and is prone to human biases. To alleviate the need for manual event ontology creation, we propose the CLUE framework for event type induction, naming, and annotation. Our main contributions in this work are: 1) designing a novel joint embedding representation for expressing both the verb-centric view and the semantic view of events; 2) event type induction using contrastive loss guided clustering; 3) event naming and refinement. Experiments demonstrate the effectiveness of our method. Our code is available at this https URL.
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https://arxiv.org/abs/2610.12580
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Natural Language to First-Order Logic LLM-based Autoformalization
2026-10-08 14:24:12Andrea Brunello, Cristian Curaba, Luca Geatti, Michele Mignani, Angelo Montanari, Nicola SaccomannoAbstract
Large Language Models (LLMs) have renewed interest in autoformalization. Yet, when First-Order Logic (FOL) is considered as the target formalism, the field still lacks a unified task formulation and a systematic survey. This paper addresses this gap: we first provide a principled definition for the FOL-autoformalization task by distinguishing Ontology Extraction from Logical Translation, showing how their conflation obscures (cross-study) evaluation; we review existing datasets, evaluation metrics, and LLM-based methods, including fine-tuning, prompting, and verification-based refinement; we identify open challenges in benchmarking, semantic evaluation, ontology-aware methods, and end-to-end applications.
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https://arxiv.org/abs/2610.12030
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Narrow and Deep: An Ontology Tower as the Knowledge of an LLM Agent for an Industrial Equipment System
2026-10-08 11:50:51Younghwan Joo, Sung-il KimAbstract
Large language model (LLM) agents are beginning to operate industrial energy equipment, and what they get right depends on what they are told about the plant. Established building ontologies name many kinds of points across many sites, whereas an industrial equipment system needs few entities with much knowledge about each. This study proposes the ontology tower, a narrow-and-deep ontology of a single equipment system whose knowledge deepens in two ways: through quantities derived from the measured points by physical relations, and through lessons from the operating journal incorporated as knowledge nodes. On a real low-humidity air-handling test plant operated daily through a programmable logic controller, agents received a text projected from its tower in a preregistered evaluation of nine tasks replayed from the plant's records, using four open-weight models from 9 to about 750 billion parameters. This knowledge raised the rate at which the agents avoided the most plausible misjudgment of each task by about 20 percentage points, and the overall task score of the 9-billion-parameter model as much as that of the largest. Operating lessons were used when incorporated into the tower or placed in the prompt as records, but seldom when left in the journal behind a search tool. In live runs through an invariant safety layer, the agents brought the controlled variable into its target band in 12 of 14 runs. An ontology narrow in entities but deep in what is known about them can thus supply the knowledge that an agent for an industrial equipment system needs.
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https://arxiv.org/abs/2610.11768
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Coverage-Aware Reasoning with Medical Tokens for Diagnosis Prediction
2026-10-07 14:39:18Kaisong Zhang, Haotian Fang, Junmeng Zhou, Hang Lv, Yulan Pan, Yanchao TanAbstract
Large language models (LLMs) offer promising potential for next-visit diagnosis prediction, owing to their ability to integrate longitudinal clinical evidence and reason over it in natural language. However, reinforcement learning for LLM reasoning commonly rewards each trajectory according to the correctness of its final answer. In next-visit diagnosis prediction, multiple diagnoses can be simultaneously valid, but independently rewarding one diagnosis per trajectory does not distinguish repeated hits from coverage of different diagnoses. The policy can therefore concentrate on a few correct diagnoses, leaving others uncovered. Meanwhile, LLM tokenizers can split ICD codes into several generic tokens with limited clinical meaning, requiring multiple decoding steps to predict each diagnosis and hindering reasoning over a large disease vocabulary. To address both challenges, we propose CARing, a framework that represents diagnoses with compositional Semantic IDs (SIDs) and optimizes reasoning trajectories for multi-label coverage. Concretely, we first encode ontology-enriched disease semantics into compact SIDs through residual quantization, and ground the resulting SID tokens in natural language and longitudinal EHR contexts through multi-task alignment and reasoning-enriched training to unlock transferable LLM reasoning. CARing further improves unordered multi-label prediction through a coverage reward for reinforcement learning and multi-positive supervision. At inference time, the model supports both efficient direct constrained decoding and multi-chain reasoning with rank fusion. On MIMIC-III and MIMIC-IV, CARing exceeds all EHR-trained baselines in weighted F1 and attains the highest top-k recall at every reported cutoff, including R@30 of 46.04% and 46.52% in reasoning mode. Our codes and logs are available at this https URL.
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https://arxiv.org/abs/2610.10641
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FaceKit: a Toolkit for Interpretable Facial Phenotyping, Synthetic Image Generation and Privacy Analysis in Rare Diseases
2026-10-07 01:43:49Hongzhuo Chen, Zhanliang Wang, Florent Pollet, Mian Umair Ahsan, Joshua Bie, Tzung-Chien Hsieh, Peter Krawitz, Cong Liu, Wendy K Chung, Chunhua Weng, Gamze G\"ursoy, Kai WangAbstract
Many rare genetic diseases are associated with recognizable craniofacial features. However, traditional approaches for describing facial morphology rely largely on qualitative clinical observation and free-text descriptions, which are often subjective, non-standardized, and difficult to reproduce across observers and institutions. Although the Human Phenotype Ontology (HPO) provides controlled terms for describing facial features, these terms are typically categorical rather than quantitative and may vary depending on examiner experience and interpretation. Here, we present FaceKit, a computational framework for quantitative facial phenotyping from frontal facial photographs. FaceKit extracts standardized measurements of facial landmarks and derived 120 morphological features, then reports feature-level z-scores representing deviation from population reference distributions. The reference distributions are built from the FairFace dataset spanning diverse ancestral groups. We evaluated FaceKit on a curated subset of the GestaltMatcher Database covering 50 rare-disease cohorts. In addition to quantitative facial analysis, FaceKit includes synthetic facial image generation to support rare disease model development and data augmentation. We also performed privacy evaluation to assess whether synthetic images reveal identifiable information from real patient photographs and could compromise patient privacy. Across disease case studies, FaceKit-derived quantitative measurements captured known facial features associated with rare genetic disorders and provided objective support for clinical phenotyping. Together, these results establish FaceKit as a useful tool for quantitative phenotyping, and has the potential to improve rare disease diagnosis, support genotype-phenotype studies, and enable more reproducible clinical characterization across diverse patient populations.
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https://arxiv.org/abs/2610.09288
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BEACON-SP: Ontology-Grounded GraphRAG Framework for Clinical Suicide Risk Assessment
2026-10-06 19:23:51Kemal Davaslioglu, Nathan Conger, Sastry Kompella, Yalin E. Sagduyu, Nathaniel D. BastianAbstract
We present BEACON-SP, an ontology-grounded Graph Retrieval-Augmented Generation (GraphRAG) framework for clinician-facing decision support in behavioral health settings such as suicide prevention, where effective assessment requires integrating heterogeneous clinical, behavioral, social, and temporal evidence. BEACON-SP combines patient knowledge graphs with ontology-guided retrieval to support multi-hop reasoning across diagnoses, medications, risk and protective factors, life events, and temporal relationships. The framework is enabled by a comprehensive suicide prevention ontology that integrates the Three-Step Theory, the Integrated Motivational-Volitional Model, and the Suicide Social Determinants of Health Ontology into a unified representation of patient risk factors. We construct ontology-grounded patient knowledge graphs and evaluate BEACON-SP for clinician-facing question answering. Compared with a vector-based retrieval-augmented generation (RAG) baseline on a 1,500-query benchmark spanning 15 clinical categories and 100 patients, BEACON-SP improves completeness, clinical relevance, and evidence grounding under a corrected comparative evaluation protocol, with a small gain on factual accuracy. In paired criterion-level comparisons, GraphRAG is preferred in 76.4% of cases. These results demonstrate the potential of ontology-guided GraphRAG to provide structured, contextualized patient evidence for clinical decision support.
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https://arxiv.org/abs/2610.09026
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Natural Language Questions as an Interface for Knowledge Graphs: QRAKEN Graph Distillation and Semantic Self-Healing
2026-10-06 10:24:26Remo Grillo, Lukas Klic, Giovanni ColavizzaAbstract
Natural-language access to RDF knowledge graphs is a core Semantic Web ambition. Large language models (LLMs) have advanced Text-to-SPARQL, yet on unfamiliar graphs they often generate valid queries that misrepresent the populated data model. QRAKEN is a training-free, ontology-agnostic neurosymbolic pipeline grounding generation in empirical graph evidence rather than schema expectations. An offline distiller produces TTQL, a compact description of populated multi-hop patterns, conditional frequencies and path-conditioned literal examples, plus a class-property co-occurrence matrix. Online, TTQL guides the LLM, while deterministic syntax, vocabulary and data-model checks provide diagnostics for iterative refinement. On CK25 (First International Text2SPARQL Challenge), under matched-condition recomputation on a QLever snapshot, QRAKEN achieves strict F1 of 0.643 $\pm$ 0.026 with GPT-4.1 mini and 0.652 $\pm$ 0.012 with GPT-5.4: relative gains of 30% and 32% over the strongest recomputed participant, outperforming systems using the same base model family. Ablations identify TTQL patterns as the dominant driver (+0.31 strict F1 over a shape-only baseline); the refinement loop provides a cheap safety net, rejecting triple patterns unsupported by the co-occurrence matrix. Compared with auto-derived SHACL, TTQL yields 64% higher strict F1, supporting the value of empirical patterns beyond schema exposure. With two local 35B 4-bit open-weight models at zero marginal cost, the same pipeline matches the strongest recomputed participant, and TTQL advantages over shape-only and SHACL baselines persist. Results on a single, relatively small benchmark provide an initial empirical signal; monolithic TTQL injection on very open cross-domain graphs remains the main limitation.
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https://arxiv.org/abs/2610.08095
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